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PloS One 2023Periodontitis is a chronic multifactorial inflammatory disease linked to oral microbiota dysbiosis. This disease progresses to infection that stimulates a host...
CONTEXT
Periodontitis is a chronic multifactorial inflammatory disease linked to oral microbiota dysbiosis. This disease progresses to infection that stimulates a host immune/inflammatory response, with progressive destruction of the tooth-supporting structures.
OBJECTIVE
This systematic review aims to present a robust critical evaluation of the evidence of salivary protein profiles for identifying oral diseases using proteomic approaches and summarize the use of these approaches to diagnose chronic periodontitis.
DATA SOURCES
A systematic literature search was conducted from January 1st, 2010, to December 1st, 2022, based on PICO criteria following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and by searching the three databases Science Direct, Scopus, and Springer Link.
STUDY SELECTION
According to the inclusion criteria, eight studies were identified to analyze the proteins identified by proteomics.
RESULTS
The protein family S100 was identified as the most abundant in patients with chronic periodontitis. In this family, an increased abundance of S100A8 and S100A9 from individuals with the active disease was observed, which strongly relates to the inflammatory response. Moreover, the ratio S100A8/S100A9 and the metalloproteinase-8 in saliva could differentiate distinct periodontitis groups. The changes in protein profile after non-surgical periodontal therapy improved the health of the buccal area. The results of this systematic review identified a set of proteins that could be used as a complementary tool for periodontitis diagnosis using salivary proteins.
CONCLUSION
Biomarkers in saliva can be used to monitor an early stage of periodontitis and the progression of the disease following therapy.
Topics: Humans; Chronic Periodontitis; Proteomics; Saliva; Periodontium; Periodontal Ligament; Calgranulin A; Calgranulin B
PubMed: 37224160
DOI: 10.1371/journal.pone.0286079 -
Journal of Nanobiotechnology Apr 2023One-third of the world's population has anemia, contributing to higher morbidity and death and impaired neurological development. Conventional anemia treatment raises... (Meta-Analysis)
Meta-Analysis
BACKGROUND
One-third of the world's population has anemia, contributing to higher morbidity and death and impaired neurological development. Conventional anemia treatment raises concerns about iron bioavailability and gastrointestinal (GI) adverse effects. This research aims to establish how iron oxide nanoparticles (IONPs) interact with probiotic cells and how they affect iron absorption, bioavailability, and microbiota variation.
METHODS
Pointing to the study of the literature and developing a review and critical synthesis, a robust search methodology was utilized by the authors. The literature search was performed in the PubMed, Scopus, and Web of Science databases. Information was collected between January 2017 and June 2022 using the PRISMA (Preferred Reporting Items for Systematic Review and Meta-Analysis) protocols for systematic reviews and meta-analyses. We identified 122 compatible research articles.
RESULTS
The research profile of the selected scientific articles revealed the efficacy of IONPs treatment carried by probiotics versus conventional treatment. Therefore, the authors employed content assessment on four topics to synthesize previous studies. The key subjects of the reviewed reports are the characteristics of the IONPs synthesis method, the evaluation of cell absorption and cytotoxicity of IONPs, and the transport of IONPs with probiotics in treating anemia.
CONCLUSIONS
To ensure a sufficient iron level in the enterocyte, probiotics with the capacity to attach to the gut wall transport IONPs into the enterocyte, where the maghemite nanoparticles are released.
Topics: Humans; Anemia; Iron; Magnetic Iron Oxide Nanoparticles; Probiotics
PubMed: 37038224
DOI: 10.1186/s12951-023-01880-9 -
International Journal of Molecular... Nov 2022Persistent organic pollutants (POPs) are organic chemical substances that are widely distributed in environments around the globe. POPs accumulate in living organisms... (Review)
Review
Persistent organic pollutants (POPs) are organic chemical substances that are widely distributed in environments around the globe. POPs accumulate in living organisms and are found at high concentrations in the food chain. Humans are thus continuously exposed to these chemical substances, in which they exert hepatic, reproductive, developmental, behavioral, neurologic, endocrine, cardiovascular, and immunologic adverse health effects. However, considerable information is unknown regarding the mechanism by which POPs exert their adverse effects in humans, as well as the molecular and cellular responses involved. Data are notably lacking concerning the consequences of acute and chronic POP exposure on changes in gene expression, protein profile, and metabolic pathways. We conducted a systematic review to provide a synthesis of knowledge of POPs arising from proteomics-based research. The data source used for this review was PubMed. This study was carried out following the PRISMA guidelines. Of the 742 items originally identified, 89 were considered in the review. This review presents a comprehensive overview of the most recent research and available solutions to explore proteomics datasets to identify new features relevant to human health. Future perspectives in proteomics studies are discussed.
Topics: Humans; Persistent Organic Pollutants; Proteomics; Environmental Pollutants; Organic Chemicals; Reproduction
PubMed: 36430748
DOI: 10.3390/ijms232214271 -
European Journal of Ophthalmology Sep 2023This review focuses on utility of artificial intelligence (AI) in analysis of biofluid markers in glaucoma. We detail the accuracy and validity of AI in the exploration...
PURPOSE
This review focuses on utility of artificial intelligence (AI) in analysis of biofluid markers in glaucoma. We detail the accuracy and validity of AI in the exploration of biomarkers to provide insight into glaucoma pathogenesis.
METHODS
A comprehensive search was conducted across five electronic databases including Embase, Medline, Cochrane Central Register of Controlled Trials, Cochrane Database of Systematic Reviews, and Web of Science. Studies pertaining to biofluid marker analysis using AI or bioinformatics in glaucoma were included. Identified studies were critically appraised and assessed for risk of bias using the Joanna Briggs Institute Critical Appraisal tools.
RESULTS
A total of 10,258 studies were screened and 39 studies met the inclusion criteria, including 23 cross-sectional studies (59%), nine prospective cohort studies (23%), six retrospective cohort studies (15%), and one case-control study (3%). Primary open angle glaucoma (POAG) was the most commonly studied subtype (55% of included studies). Twenty-four studies examined disease characteristics, 10 explored treatment decisions, and 5 provided diagnostic clarification. While studies examined at entire metabolomic or proteomic profiles to determine changes in POAG, there was heterogeneity in the data with over 175 unique, differentially expressed biomarkers reported. Discriminant analysis and artificial neural network predictive models displayed strong differentiating ability between glaucoma patients and controls, although these tools were untested in a clinical context.
CONCLUSION
The use of AI models could inform glaucoma diagnosis with high sensitivity and specificity. While insight into differentially expressed biomarkers is valuable in pathogenic exploration, no clear pathogenic mechanism in glaucoma has emerged.
Topics: Humans; Artificial Intelligence; Biomarkers; Case-Control Studies; Cross-Sectional Studies; Glaucoma; Glaucoma, Open-Angle; Prospective Studies; Proteomics; Retrospective Studies
PubMed: 36426575
DOI: 10.1177/11206721221140948 -
Iranian Journal of Otorhinolaryngology Jul 2022After more than a year of the COVID-19 pandemic, audio-vestibular problems have been reported as consequences. Several limited case report studies with different...
INTRODUCTION
After more than a year of the COVID-19 pandemic, audio-vestibular problems have been reported as consequences. Several limited case report studies with different methodologies were published. This study aimed to describe the impact of COVID-19 on the auditory-vestibular system and communication problems in subjects with hearing impairment.
MATERIALS AND METHODS
The current systematic review was performed based on the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) guideline. PubMed, Web of Science, and Google Scholar were searched to find relevant articles using combined keywords.
RESULTS
Out of 26 final studies, 20 studies dealt with the effects of COVID-19 on the auditory and vestibular system, and six articles examined the COVID-19 effects on hearing-impaired people and patients. In these studies, dizziness (17.8%), tinnitus (8.1%), and vertigo (2.8%) were common symptoms. Most studies were case reports (42.30%), and in terms of quality, nine studies (34.61%) were in the suitable quality group.
CONCLUSIONS
COVID-19 might cause auditory-vestibular system problems by directly affecting the structures or functions of the inner ear or by weakening the immune system. The need for taking preventive measures during the COVID-19 pandemic has caused communication and social challenges, particularly for people with hearing loss.
PubMed: 36035653
DOI: 10.22038/IJORL.2022.60404.3079 -
Frontiers in Endocrinology 2022Diabetic nephropathy (DN) is a major microvascular complication of both type 1 and type 2 diabetes mellitus and is the most frequent cause of end-stage renal disease... (Meta-Analysis)
Meta-Analysis
Diabetic nephropathy (DN) is a major microvascular complication of both type 1 and type 2 diabetes mellitus and is the most frequent cause of end-stage renal disease with an increasing prevalence. Presently there is no non-invasive method for differential diagnosis, and an efficient target therapy is lacking. Extracellular vesicles (EV), including exosomes, microvesicles, and apoptotic bodies, are present in various body fluids such as blood, cerebrospinal fluid, and urine. Proteins in EV are speculated to be involved in various processes of disease and reflect the original cells' physiological states and pathological conditions. This systematic review is based on urinary extracellular vesicles studies, which enrolled patients with DN and investigated the proteins in urinary EV. We systematically reviewed articles from the PubMed, Embase, Web of Science databases, and China National Knowledge Infrastructure (CNKI) database until January 4, 2022. The article quality was appraised according to the Newcastle-Ottawa Quality Assessment Scale (NOS). The methodology of samples, isolation and purification techniques of urinary EV, and characterization methods are summarized. Molecular functions, biological processes, and pathways were enriched in all retrievable urinary EV proteins. Protein-protein interaction analysis (PPI) revealed pathways of potential biomarkers. A total of 539 articles were retrieved, and 13 eligible records were enrolled in this systematic review and meta-analysis. And two studies performed mass spectrometry to obtain the proteome profile. Two of them enrolled only T1DM patients, two studies enrolled both patients with T1DM and T2DM, and other the nine studies focused on T2DM patients. In total 988 participants were enrolled, and DN was diagnosed according to UACR, UAER, or decreased GFR. Totally 579 urinary EV proteins were detected and 28 of them showed a potential value to be biomarkers. The results of bioinformatics analysis revealed that urinary EV may participate in DN through various pathways such as angiogenesis, biogenesis of EV, renin-angiotensin system, fluid shear stress and atherosclerosis, collagen degradation, and immune system. Besides that, it is necessary to report results compliant with the guideline of ISEV, in orderto assure repeatability and help for further studies. This systematic review concordance with previous studies and the results of meta-analysis may help to value the methodology details when urinary EV proteins were reported, and also help to deepen the understanding of urinary EV proteins in DN.
Topics: Biomarkers; Diabetes Mellitus, Type 1; Diabetes Mellitus, Type 2; Diabetic Nephropathies; Extracellular Vesicles; Humans; Proteome
PubMed: 36034457
DOI: 10.3389/fendo.2022.866252 -
Fertility and Sterility Aug 2022To identify the most robust molecular biomarkers in sperm and seminal plasma for the diagnosis of male infertility, and to evaluate their clinical use. (Review)
Review
OBJECTIVE
To identify the most robust molecular biomarkers in sperm and seminal plasma for the diagnosis of male infertility, and to evaluate their clinical use.
DESIGN
Systematic review.
SETTING
Not applicable.
PATIENT(S)
Accessible studies reporting well-defined (in)fertile populations and semen molecular biomarkers were included in this review.
INTERVENTION(S)
A systematic search of the literature published in MEDLINE-PubMed and EMBASE databases was performed, following Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.
MAIN OUTCOME MEASURE(S)
The primary outcome was the content, expression, or activity of molecular biomarkers in human semen samples. Only studies reporting a receiver-operating characteristic (ROC) analysis values were included.
RESULT(S)
Eighty-nine studies were included. Direct evaluation of sperm DNA damage has high potential as a diagnostic biomarker of fertility and assisted reproductive technology outcomes (area under the curve [AUCs] median = 0.67). Regarding strand break-associated chromatin modifications, γH2AX levels show good predictive value for the diagnosis of male infertility (AUCs median = 0.93). Some noncoding ribonucleic acid (RNA) exhibit excellent predictive values; miR-34c-5p in semen is the most well-characterized and robust transcriptomic biomarker (AUCs median = 0.78). While many proteins in semen show fair diagnostic value for sperm quality and fertilizing capacity, the levels of some, such as TEX101, in seminal plasma have an excellent diagnostic potential (AUCs median = 0.69). Although individual metabolites and metabolomic profiles in seminal plasma present good predictive value, the latter seem to be better than the former when inferring sperm quality and fertilizing capacity.
CONCLUSION(S)
The current review supports that some Omics (e.g., DNA structure and integrity, genomics and epigenomics, transcriptomics, metabolomics, and proteomics) could be considered relevant molecular biomarkers that may help identify infertility etiologies and fertilization prognosis with cost-effective, simple, and accurate diagnosis.
Topics: Biomarkers; Fertility; Humans; Infertility, Male; Male; Semen; Semen Analysis; Spermatozoa
PubMed: 35718545
DOI: 10.1016/j.fertnstert.2022.04.028 -
Environment International Jun 2022Systematic evidence maps are increasingly used to develop chemical risk assessments. These maps can provide an overview of available studies and relevant study... (Review)
Review
BACKGROUND
Systematic evidence maps are increasingly used to develop chemical risk assessments. These maps can provide an overview of available studies and relevant study information to be used for various research objectives and applications. Environmental epidemiological studies that examine the impact of chemical exposures on various 'omic profiles in human populations provide relevant mechanistic information and can be used for benchmark dose modeling to derive potential human health reference values.
OBJECTIVES
To create a systematic evidence map of environmental epidemiological studies examining environmental contaminant exposures with 'omics in order to characterize the extent of available studies for future research needs.
METHODS
Systematic review methods were used to search and screen the literature and included the use of machine learning methods to facilitate screening studies. The Populations, Exposures, Comparators and Outcomes (PECO) criteria were developed to identify and screen relevant studies. Studies that met the PECO criteria after full-text review were summarized with information such as study population, study design, sample size, exposure measurement, and 'omics analysis.
RESULTS
Over 10,000 studies were identified from scientific databases. Screening processes were used to identify 84 studies considered PECO-relevant after full-text review. Various contaminants (e.g. phthalate, benzene, arsenic, etc.) were investigated in epidemiological studies that used one or more of the four 'omics of interest: epigenomics, transcriptomics, proteomics, and metabolomics . The epidemiological study designs that were used to explore single or integrated 'omic research questions with contaminant exposures were cohort studies, controlled trials, cross-sectional, and case-control studies. An interactive web-based systematic evidence map was created to display more study-related information.
CONCLUSIONS
This systematic evidence map is a novel tool to visually characterize the available environmental epidemiological studies investigating contaminants and biological effects using 'omics technology and serves as a resource for investigators and allows for a range of applications in chemical research and risk assessment needs.
Topics: Cross-Sectional Studies; Environmental Exposure; Epidemiologic Studies; Humans; Reference Values; Risk Assessment
PubMed: 35551006
DOI: 10.1016/j.envint.2022.107243 -
Biomolecules Mar 2022Proteases and protease inhibitors (P/PIs) are involved in many biological processes in human skin, yet often only specific families or related groups of P/PIs are...
Proteases and protease inhibitors (P/PIs) are involved in many biological processes in human skin, yet often only specific families or related groups of P/PIs are investigated. Proteomics approaches, such as mass spectrometry, can define proteome signatures (including P/PIs) in tissues; however, they struggle to detect low-abundance proteins. To overcome these issues, we aimed to produce a comprehensive proteome of all P/PIs present in normal and diseased human skin, in vivo, by carrying out a modified systematic review using a list of P/PIs from MEROPS and combining this with key search terms in Web of Science. Resulting articles were manually reviewed against inclusion/exclusion criteria and a dataset constructed. This study identified 111 proteases and 77 protease inhibitors in human skin, comprising the serine, metallo-, cysteine and aspartic acid catalytic families of proteases. P/PIs showing no evidence of catalytic activity or protease inhibition, were designated non-peptidase homologs (NPH), and no reported protease inhibitory activity (NRPIA), respectively. MMP9 and TIMP1 were the most frequently published P/PIs and were reported in normal skin and most skin disease groups. Normal skin and diseased skin showed significant overlap with respect to P/PI profile; however, MMP23 was identified in several skin disease groups, but was absent in normal skin. The catalytic profile of P/PIs in wounds, scars and solar elastosis was distinct from normal skin, suggesting that a different group of P/PIs is responsible for disease progression. In conclusion, this study uses a novel approach to provide a comprehensive inventory of P/PIs in normal and diseased human skin reported in our database. The database may be used to determine either which P/PIs are present in specific diseases or which diseases individual P/PIs may influence.
Topics: Antiviral Agents; Humans; Peptide Hydrolases; Protease Inhibitors; Proteome; Proteomics
PubMed: 35327667
DOI: 10.3390/biom12030475 -
Biomedicines Jan 2022Several biologic therapies that target inflammatory modulators are now used for treating patients with uncontrolled, severe asthma. Knowledge about how this type of... (Review)
Review
Several biologic therapies that target inflammatory modulators are now used for treating patients with uncontrolled, severe asthma. Knowledge about how this type of treatment modifies the molecular milieu is rapidly increasing. Thus, this systematic review aimed to compile the reported effects of therapeutic antibodies on the transcriptome or proteome of asthma patients. Studies of asthmatic patients under biological treatment describing transcriptomic or proteomic changes upon treatment were included. Preclinical or single gene/protein studies were not considered. PubMed and Scopus search was performed in August and September 2021. Following PRISMA guidelines and GRADE recommendations, we selected 12 studies on gene or protein expression changes in patients treated with the antibodies currently approved by EMA and the FDA. All studies were at low risk of bias as per the RoB2 tool. Different gene clusters have been identified to change upon omalizumab treatment, found a reduction in eosinophil-associated gene signatures after benralizumab treatment, and protein profiles were different in patients treated with mepolizumab and in those treated with benralizumab. The main potential biomarkers proposed by the selected studies are shown. These results may contribute to discovering biomarkers of response and selecting the best therapy for each patient.
PubMed: 35203504
DOI: 10.3390/biomedicines10020293